Use when building large Bowtie 2 index files from reference sequences for alignment of reads to large genomes (>4 billion bases).
Builds large-format Bowtie 2 index files (.bt2l extension) from FASTA reference sequences for use with bowtie2-align-l.
bowtie2-build-l [options] <reference_in> <bt2_index_base>/home/vimalinx/miniforge3/envs/bio/bin/bowtie2-build-lbowtie2-build-l when the reference is large enough that you need Bowtie 2 large-index output (.bt2l).bowtie2-align-l or a wrapper that resolves to the large-index path.-c when sequences are provided directly on the command line.bowtie2-build unless they intentionally need to force the large-index builder.# Build a large Bowtie 2 index from one FASTA
bowtie2-build-l ref.fa ref_large
# Build from multiple FASTA files
bowtie2-build-l ref1.fa,ref2.fa ref_large
# Use multiple threads during index construction
bowtie2-build-l --threads 8 ref.fa ref_large
# Build from literal reference sequence text
bowtie2-build-l -c ACGTACGT,GGGTTTAA ref_large
bowtie2-build-l <reference.fasta> <index_basename> to generate index files.bt2l files were created with the specified basenamebowtie2 -x <index_basename> for alignmentbowtie2-build wrapper instead, as recommended by the tool warning--threads to parallelize builds on multi-core systems for faster processing-x without adding .bt2l suffixes manually